#!/bin/bash

# Paratmers.
segidx=/data2/projects/huref_scaffold/segemehl_idxs/huref_contigs.idx
ref=/data2/assemblies/human/hs_alt_contigs.fasta
out_dir=/data2/projects/huref_scaffold/sanger_verify
query_dir=/data2/projects/huref_scaffold/assemblies/read_4_0

# Loop over queries.
for x in $(ls $query_dir); do
	# Make names.
	bname=$(basename $x .fasta)
	query=${query_dir}/$x
	output=${out_dir}/${bname}.txt
	
	# Run verify.
	segemehl.x -i $segidx -d $ref -q $query -t 30 > $output
done;

